CITY is constructed by the IPUMS-USA team using PUMAs as building blocks. Since the 2012 and (in progress) 2013 multi-year files actually contain two distinct sets of PUMA codes and boundaries, these constructions are more difficult. The Census Bureau has been delineating new sets of PUMAs every 10 years since 1990, with the most recent set of PUMAs being generated for the 2010 Decennial Census. The 2012 ACS was the first ACS to use these new PUMAs, meaning that the previous years that are combined with 2012 and 2013 to form the multi-year files are composed of the older PUMAs.

Since CITY is available for each of the 1-year files from 2009-2013, you can create a 2013 5-year ACS file that contains the CITY variable. You can follow the instructions found in this previous answer for creating a 5-year ACS file for 2013. In addition, you will want to include the CITY variable in each of your 1-year samples. Note that if a CITY is identifiable in 2012/2013 but is not identifiable in 2011/earlier, this will also be true in your multi-year file. As mentioned earlier, remember that the PUMA definitions used to create the 2012 and 2013 CITY variable differ from the previous ACS samples; thus, they are not perfectly comparable.